Starting phenix.real_space_refine on Thu Feb 15 20:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dyr_30923/02_2024/7dyr_30923.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8667 2.51 5 N 2229 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 2": "OE1" <-> "OE2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y ARG 202": "NH1" <-> "NH2" Residue "Y ARG 247": "NH1" <-> "NH2" Residue "Z ARG 54": "NH1" <-> "NH2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z GLU 94": "OE1" <-> "OE2" Residue "Z ARG 96": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z GLU 193": "OE1" <-> "OE2" Residue "Z ARG 221": "NH1" <-> "NH2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "Z" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "G" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.50, per 1000 atoms: 0.56 Number of scatterers: 13326 At special positions: 0 Unit cell: (120.954, 128.381, 85.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2349 8.00 N 2229 7.00 C 8667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.5 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 3 sheets defined 77.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 117 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP Y 129 " --> pdb=" O ASP Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL Y 151 " --> pdb=" O GLN Y 147 " (cutoff:3.500A) Proline residue: Y 154 - end of helix removed outlier: 3.808A pdb=" N ALA Y 159 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 171 removed outlier: 3.727A pdb=" N ASN Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL Y 191 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 Processing helix chain 'Z' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O GLN Z 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Z 24 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 99 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.512A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 183 No H-bonds generated for 'chain 'Z' and resid 181 through 183' Processing helix chain 'Z' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR Z 211 " --> pdb=" O VAL Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 242 Processing helix chain 'Z' and resid 244 through 260 Processing helix chain 'Z' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.543A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.808A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 192 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.595A pdb=" N HIS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.512A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.869A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.808A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 192 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG F 22 " --> pdb=" O GLN F 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.716A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.512A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 244 through 260 Processing helix chain 'F' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR Z 232 " --> pdb=" O VAL Z 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR C 232 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR F 232 " --> pdb=" O VAL F 219 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 2665 1.46 - 1.58: 6509 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 13590 Sorted by residual: bond pdb=" N GLN F 41 " pdb=" CA GLN F 41 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.59e+00 bond pdb=" N GLN C 41 " pdb=" CA GLN C 41 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" CB PRO Z 132 " pdb=" CG PRO Z 132 " ideal model delta sigma weight residual 1.492 1.406 0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.92e+00 bond pdb=" CB PRO F 132 " pdb=" CG PRO F 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.91e+00 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.58: 407 106.58 - 113.50: 7725 113.50 - 120.42: 5520 120.42 - 127.34: 4699 127.34 - 134.27: 147 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N VAL E 156 " pdb=" CA VAL E 156 " pdb=" C VAL E 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL Y 156 " pdb=" CA VAL Y 156 " pdb=" C VAL Y 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL B 156 " pdb=" CA VAL B 156 " pdb=" C VAL B 156 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" C GLN Z 41 " pdb=" CA GLN Z 41 " pdb=" CB GLN Z 41 " ideal model delta sigma weight residual 111.48 105.78 5.70 1.59e+00 3.96e-01 1.29e+01 angle pdb=" CA TYR A 73 " pdb=" CB TYR A 73 " pdb=" CG TYR A 73 " ideal model delta sigma weight residual 113.90 107.46 6.44 1.80e+00 3.09e-01 1.28e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7076 17.78 - 35.56: 650 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7953 sinusoidal: 2979 harmonic: 4974 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N PRO B 175 " pdb=" CA PRO B 175 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE Y 174 " pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1715 0.052 - 0.104: 424 0.104 - 0.157: 78 0.157 - 0.209: 8 0.209 - 0.261: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CA ASP Z 103 " pdb=" N ASP Z 103 " pdb=" C ASP Z 103 " pdb=" CB ASP Z 103 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2223 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Y 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 71 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 72 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.050 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2180 2.74 - 3.28: 13533 3.28 - 3.82: 22248 3.82 - 4.36: 26647 4.36 - 4.90: 46236 Nonbonded interactions: 110844 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 125 " pdb=" NH2 ARG Z 39 " model vdw 2.205 2.520 nonbonded pdb=" OD2 ASP E 125 " pdb=" NH2 ARG F 39 " model vdw 2.205 2.520 nonbonded pdb=" OD2 ASP B 125 " pdb=" NH2 ARG C 39 " model vdw 2.206 2.520 nonbonded pdb=" N ASN G 67 " pdb=" OD1 ASN G 67 " model vdw 2.275 2.520 nonbonded pdb=" N ASN D 67 " pdb=" OD1 ASN D 67 " model vdw 2.275 2.520 ... (remaining 110839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.380 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.370 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13590 Z= 0.508 Angle : 0.779 9.857 18498 Z= 0.420 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.368 88.905 4797 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 3.56 % Allowed : 20.33 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 138 HIS 0.004 0.001 HIS Y 122 PHE 0.011 0.001 PHE C 47 TYR 0.027 0.003 TYR A 73 ARG 0.004 0.000 ARG Z 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 285 time to evaluate : 1.544 Fit side-chains REVERT: Y 26 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Y 64 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: Y 125 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: Y 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tm-30) REVERT: Z 17 THR cc_start: 0.7504 (m) cc_final: 0.7291 (p) REVERT: Z 38 GLU cc_start: 0.8653 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 60 ASN cc_start: 0.6699 (m-40) cc_final: 0.6131 (t0) REVERT: Z 73 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6989 (mt-10) REVERT: Z 94 GLU cc_start: 0.7693 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 175 LYS cc_start: 0.7153 (tptm) cc_final: 0.6931 (tptp) REVERT: Z 223 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7239 (m) REVERT: Z 230 HIS cc_start: 0.7483 (m90) cc_final: 0.7028 (m90) REVERT: A 50 ASP cc_start: 0.6889 (m-30) cc_final: 0.6620 (m-30) REVERT: A 55 ASN cc_start: 0.8150 (p0) cc_final: 0.7944 (p0) REVERT: B 26 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 64 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 125 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (m-30) REVERT: B 201 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtp) REVERT: C 15 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7833 (ptpp) REVERT: C 17 THR cc_start: 0.7845 (m) cc_final: 0.7635 (p) REVERT: C 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7260 (m-30) REVERT: C 22 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6116 (mtm110) REVERT: C 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8073 (tt0) REVERT: C 60 ASN cc_start: 0.6867 (m-40) cc_final: 0.6507 (t0) REVERT: C 73 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 50 ASP cc_start: 0.7159 (m-30) cc_final: 0.6647 (m-30) REVERT: D 55 ASN cc_start: 0.8316 (p0) cc_final: 0.7979 (p0) REVERT: E 3 ILE cc_start: 0.7863 (mt) cc_final: 0.7514 (mm) REVERT: E 4 THR cc_start: 0.7488 (p) cc_final: 0.7264 (t) REVERT: E 130 ASN cc_start: 0.8118 (m110) cc_final: 0.7796 (m-40) REVERT: E 142 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 176 GLU cc_start: 0.7063 (tp30) cc_final: 0.6785 (tm-30) REVERT: E 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7495 (m-40) REVERT: E 244 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7980 (ttpp) REVERT: F 17 THR cc_start: 0.7743 (m) cc_final: 0.7460 (p) REVERT: F 38 GLU cc_start: 0.8654 (tt0) cc_final: 0.8036 (tt0) REVERT: F 60 ASN cc_start: 0.6881 (m-40) cc_final: 0.6221 (t0) REVERT: F 73 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 95 GLN cc_start: 0.7180 (mp10) cc_final: 0.6768 (mp-120) REVERT: F 102 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6931 (mm) REVERT: F 108 ASN cc_start: 0.7986 (m-40) cc_final: 0.7752 (m-40) REVERT: F 189 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: F 193 GLU cc_start: 0.7609 (tt0) cc_final: 0.7397 (tt0) REVERT: F 259 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6457 (ttp80) REVERT: F 281 CYS cc_start: 0.7790 (m) cc_final: 0.7579 (m) REVERT: G 19 TRP cc_start: 0.6334 (t60) cc_final: 0.6107 (t60) outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 1.1635 time to fit residues: 403.5914 Evaluate side-chains 241 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 MET Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 29 ASN ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN A 42 GLN C 108 ASN C 158 ASN D 15 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.249 Angle : 0.611 6.402 18498 Z= 0.324 Chirality : 0.042 0.174 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.888 54.054 1970 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 3.63 % Allowed : 16.99 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1773 helix: 1.35 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 127 HIS 0.003 0.001 HIS Z 71 PHE 0.012 0.001 PHE C 157 TYR 0.026 0.002 TYR A 73 ARG 0.004 0.001 ARG Z 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7687 (t) cc_final: 0.7439 (p) REVERT: Y 125 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: Z 38 GLU cc_start: 0.8708 (tt0) cc_final: 0.8064 (tt0) REVERT: Z 223 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7075 (m) REVERT: Z 230 HIS cc_start: 0.7337 (m90) cc_final: 0.6892 (m90) REVERT: Z 259 ARG cc_start: 0.6787 (ttm110) cc_final: 0.6521 (ttp80) REVERT: A 55 ASN cc_start: 0.8085 (p0) cc_final: 0.7847 (p0) REVERT: B 26 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 125 ASP cc_start: 0.7131 (m-30) cc_final: 0.6685 (m-30) REVERT: B 244 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7632 (ttpp) REVERT: C 15 LYS cc_start: 0.8080 (ptpp) cc_final: 0.7864 (ptpp) REVERT: C 17 THR cc_start: 0.7944 (m) cc_final: 0.7539 (p) REVERT: C 38 GLU cc_start: 0.8622 (tt0) cc_final: 0.8135 (tt0) REVERT: C 60 ASN cc_start: 0.6555 (m-40) cc_final: 0.6071 (t0) REVERT: C 73 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7011 (mt-10) REVERT: E 176 GLU cc_start: 0.7042 (tp30) cc_final: 0.6671 (tm-30) REVERT: E 244 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7917 (ttpp) REVERT: F 29 ASN cc_start: 0.8072 (m-40) cc_final: 0.7868 (m110) REVERT: F 38 GLU cc_start: 0.8688 (tt0) cc_final: 0.8122 (tt0) REVERT: F 60 ASN cc_start: 0.6960 (m-40) cc_final: 0.6348 (t0) REVERT: F 95 GLN cc_start: 0.7036 (mp10) cc_final: 0.6648 (mp-120) REVERT: F 183 MET cc_start: 0.6473 (mmm) cc_final: 0.6158 (mmm) REVERT: F 189 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: F 281 CYS cc_start: 0.7818 (m) cc_final: 0.7505 (m) outliers start: 50 outliers final: 17 residues processed: 272 average time/residue: 1.2047 time to fit residues: 357.8484 Evaluate side-chains 237 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN A 11 ASN A 15 ASN C 108 ASN D 11 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.258 Angle : 0.602 8.032 18498 Z= 0.317 Chirality : 0.042 0.180 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.470 51.168 1955 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.34 % Allowed : 17.65 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1773 helix: 1.42 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 127 HIS 0.003 0.001 HIS Z 71 PHE 0.012 0.001 PHE F 47 TYR 0.028 0.002 TYR A 73 ARG 0.003 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7711 (t) cc_final: 0.7505 (p) REVERT: Y 125 ASP cc_start: 0.7133 (m-30) cc_final: 0.6684 (m-30) REVERT: Y 176 GLU cc_start: 0.7135 (tp30) cc_final: 0.6719 (tm-30) REVERT: Z 38 GLU cc_start: 0.8724 (tt0) cc_final: 0.8146 (tt0) REVERT: Z 94 GLU cc_start: 0.7387 (tt0) cc_final: 0.7048 (tt0) REVERT: Z 223 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.6998 (m) REVERT: A 55 ASN cc_start: 0.7977 (p0) cc_final: 0.7729 (p0) REVERT: B 26 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 125 ASP cc_start: 0.7140 (m-30) cc_final: 0.6714 (m-30) REVERT: C 15 LYS cc_start: 0.8064 (ptpp) cc_final: 0.7854 (ptpp) REVERT: C 38 GLU cc_start: 0.8575 (tt0) cc_final: 0.8123 (tt0) REVERT: C 73 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6928 (mt-10) REVERT: D 29 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5681 (tm) REVERT: E 64 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: E 73 ASP cc_start: 0.8032 (t70) cc_final: 0.7822 (t70) REVERT: E 176 GLU cc_start: 0.7060 (tp30) cc_final: 0.6652 (tm-30) REVERT: E 244 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7913 (ttpp) REVERT: F 29 ASN cc_start: 0.7972 (m-40) cc_final: 0.7755 (m110) REVERT: F 38 GLU cc_start: 0.8690 (tt0) cc_final: 0.8168 (tt0) REVERT: F 95 GLN cc_start: 0.7106 (mp10) cc_final: 0.6777 (mp-120) REVERT: F 183 MET cc_start: 0.6499 (mmm) cc_final: 0.6143 (mmm) REVERT: F 189 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6223 (pt0) REVERT: F 281 CYS cc_start: 0.7803 (m) cc_final: 0.7495 (m) REVERT: G 19 TRP cc_start: 0.6322 (t60) cc_final: 0.6022 (t60) outliers start: 46 outliers final: 23 residues processed: 263 average time/residue: 1.2298 time to fit residues: 352.9544 Evaluate side-chains 247 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 140 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN A 15 ASN C 108 ASN D 11 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13590 Z= 0.221 Angle : 0.573 8.288 18498 Z= 0.302 Chirality : 0.041 0.172 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.314 56.812 1953 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.27 % Allowed : 17.72 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1773 helix: 1.59 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 127 HIS 0.002 0.001 HIS Z 71 PHE 0.012 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.003 0.000 ARG Z 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 233 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7690 (t) cc_final: 0.7487 (p) REVERT: Y 125 ASP cc_start: 0.7208 (m-30) cc_final: 0.6225 (m-30) REVERT: Y 176 GLU cc_start: 0.7197 (tp30) cc_final: 0.6686 (tm-30) REVERT: Z 38 GLU cc_start: 0.8701 (tt0) cc_final: 0.8482 (tt0) REVERT: Z 94 GLU cc_start: 0.7377 (tt0) cc_final: 0.7041 (tt0) REVERT: Z 223 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.6968 (m) REVERT: A 16 ASN cc_start: 0.7604 (m110) cc_final: 0.7369 (m-40) REVERT: A 55 ASN cc_start: 0.7885 (p0) cc_final: 0.7622 (p0) REVERT: B 26 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7103 (mm-30) REVERT: B 125 ASP cc_start: 0.7143 (m-30) cc_final: 0.6647 (m-30) REVERT: C 15 LYS cc_start: 0.8058 (ptpp) cc_final: 0.7849 (ptpp) REVERT: C 38 GLU cc_start: 0.8558 (tt0) cc_final: 0.8134 (tt0) REVERT: D 29 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5898 (tm) REVERT: E 176 GLU cc_start: 0.7028 (tp30) cc_final: 0.6571 (tm-30) REVERT: E 244 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7856 (ttpp) REVERT: F 14 LYS cc_start: 0.7109 (mtmp) cc_final: 0.6899 (mppt) REVERT: F 38 GLU cc_start: 0.8687 (tt0) cc_final: 0.8207 (tt0) REVERT: F 95 GLN cc_start: 0.7026 (mp10) cc_final: 0.6660 (mp-120) REVERT: F 183 MET cc_start: 0.6483 (mmm) cc_final: 0.6147 (mmm) REVERT: F 189 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6197 (pt0) REVERT: F 281 CYS cc_start: 0.7674 (m) cc_final: 0.7383 (m) REVERT: G 19 TRP cc_start: 0.6359 (t60) cc_final: 0.6015 (t60) outliers start: 45 outliers final: 25 residues processed: 264 average time/residue: 1.1716 time to fit residues: 339.1688 Evaluate side-chains 249 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 0.0020 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN Z 61 ASN A 15 ASN B 180 ASN C 108 ASN F 29 ASN F 108 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13590 Z= 0.297 Angle : 0.618 8.011 18498 Z= 0.327 Chirality : 0.043 0.194 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.448 59.997 1952 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.82 % Favored : 93.01 % Rotamer: Outliers : 3.49 % Allowed : 17.72 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1773 helix: 1.61 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.42 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 127 HIS 0.003 0.001 HIS Z 71 PHE 0.015 0.002 PHE F 47 TYR 0.030 0.002 TYR A 73 ARG 0.003 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 223 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7733 (t) cc_final: 0.7436 (p) REVERT: Y 47 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7123 (mtmt) REVERT: Y 58 MET cc_start: 0.7768 (mmm) cc_final: 0.7441 (mmp) REVERT: Y 125 ASP cc_start: 0.7164 (m-30) cc_final: 0.6186 (m-30) REVERT: Z 54 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7319 (ttm170) REVERT: Z 94 GLU cc_start: 0.7380 (tt0) cc_final: 0.7061 (tt0) REVERT: Z 187 PHE cc_start: 0.7338 (t80) cc_final: 0.7043 (t80) REVERT: Z 223 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7064 (m) REVERT: A 29 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5951 (tm) REVERT: A 55 ASN cc_start: 0.7939 (p0) cc_final: 0.7679 (p0) REVERT: B 26 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 125 ASP cc_start: 0.7151 (m-30) cc_final: 0.6670 (m-30) REVERT: C 38 GLU cc_start: 0.8569 (tt0) cc_final: 0.8150 (tt0) REVERT: C 129 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7723 (m) REVERT: D 29 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5802 (tm) REVERT: E 47 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7366 (tttt) REVERT: E 64 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: E 176 GLU cc_start: 0.7082 (tp30) cc_final: 0.6599 (tm-30) REVERT: E 244 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7847 (ttpp) REVERT: F 38 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: F 60 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6082 (m-40) REVERT: F 95 GLN cc_start: 0.6990 (mp10) cc_final: 0.6632 (mp-120) REVERT: F 183 MET cc_start: 0.6511 (mmm) cc_final: 0.6141 (mmm) REVERT: F 189 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6180 (pt0) REVERT: F 281 CYS cc_start: 0.7655 (m) cc_final: 0.7365 (m) REVERT: G 19 TRP cc_start: 0.6459 (t60) cc_final: 0.6065 (t60) outliers start: 48 outliers final: 24 residues processed: 257 average time/residue: 1.2473 time to fit residues: 350.2228 Evaluate side-chains 250 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 41 optimal weight: 0.0370 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN Z 61 ASN A 15 ASN A 16 ASN C 98 ASN C 108 ASN D 11 ASN F 108 ASN F 189 GLN G 11 ASN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.231 Angle : 0.581 7.191 18498 Z= 0.306 Chirality : 0.041 0.176 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.346 55.664 1952 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.49 % Allowed : 17.65 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1773 helix: 1.75 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.002 0.001 HIS Z 71 PHE 0.013 0.001 PHE F 47 TYR 0.025 0.002 TYR A 73 ARG 0.002 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7721 (t) cc_final: 0.7439 (p) REVERT: Y 47 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7182 (mtmt) REVERT: Y 58 MET cc_start: 0.7779 (mmm) cc_final: 0.7536 (mmp) REVERT: Y 125 ASP cc_start: 0.7138 (m-30) cc_final: 0.6086 (m-30) REVERT: Y 244 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7453 (ttpp) REVERT: Z 54 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7327 (ttm170) REVERT: Z 66 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6841 (mt0) REVERT: Z 94 GLU cc_start: 0.7371 (tt0) cc_final: 0.7075 (tt0) REVERT: Z 187 PHE cc_start: 0.7184 (t80) cc_final: 0.6931 (t80) REVERT: A 29 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5983 (tm) REVERT: A 55 ASN cc_start: 0.7867 (p0) cc_final: 0.7594 (p0) REVERT: B 26 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7103 (mm-30) REVERT: B 73 ASP cc_start: 0.7869 (t70) cc_final: 0.7643 (OUTLIER) REVERT: B 125 ASP cc_start: 0.7120 (m-30) cc_final: 0.6682 (m-30) REVERT: C 38 GLU cc_start: 0.8541 (tt0) cc_final: 0.8141 (tt0) REVERT: C 129 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7776 (m) REVERT: D 29 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5753 (tm) REVERT: E 64 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8096 (mtp) REVERT: E 176 GLU cc_start: 0.6991 (tp30) cc_final: 0.6496 (tm-30) REVERT: E 244 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7855 (ttpp) REVERT: F 14 LYS cc_start: 0.7068 (mtmp) cc_final: 0.6840 (mppt) REVERT: F 38 GLU cc_start: 0.8676 (tt0) cc_final: 0.8191 (tt0) REVERT: F 60 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.5817 (m-40) REVERT: F 95 GLN cc_start: 0.6974 (mp10) cc_final: 0.6624 (mp-120) REVERT: F 183 MET cc_start: 0.6531 (mmm) cc_final: 0.6154 (mmm) REVERT: F 189 GLN cc_start: 0.6527 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: F 281 CYS cc_start: 0.7620 (m) cc_final: 0.7350 (m) REVERT: G 19 TRP cc_start: 0.6398 (t60) cc_final: 0.6004 (t60) outliers start: 48 outliers final: 29 residues processed: 259 average time/residue: 1.2664 time to fit residues: 358.5238 Evaluate side-chains 255 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN Z 61 ASN A 15 ASN A 42 GLN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.253 Angle : 0.597 10.349 18498 Z= 0.314 Chirality : 0.042 0.180 2226 Planarity : 0.006 0.090 2328 Dihedral : 5.345 56.363 1952 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.82 % Favored : 93.01 % Rotamer: Outliers : 3.56 % Allowed : 18.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1773 helix: 1.78 (0.15), residues: 1323 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS Z 71 PHE 0.014 0.001 PHE F 47 TYR 0.026 0.002 TYR A 73 ARG 0.002 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 223 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7730 (t) cc_final: 0.7442 (p) REVERT: Y 47 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7203 (mtmt) REVERT: Y 58 MET cc_start: 0.7795 (mmm) cc_final: 0.7527 (mmp) REVERT: Y 125 ASP cc_start: 0.7101 (m-30) cc_final: 0.6070 (m-30) REVERT: Y 244 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7538 (ttpp) REVERT: Z 54 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7304 (ttm170) REVERT: Z 66 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6854 (mt0) REVERT: Z 94 GLU cc_start: 0.7336 (tt0) cc_final: 0.7006 (tt0) REVERT: Z 187 PHE cc_start: 0.7308 (t80) cc_final: 0.7041 (t80) REVERT: A 55 ASN cc_start: 0.7851 (p0) cc_final: 0.7584 (p0) REVERT: B 26 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 73 ASP cc_start: 0.7859 (t70) cc_final: 0.7612 (t70) REVERT: B 125 ASP cc_start: 0.7123 (m-30) cc_final: 0.6686 (m-30) REVERT: C 38 GLU cc_start: 0.8537 (tt0) cc_final: 0.8138 (tt0) REVERT: C 129 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7812 (m) REVERT: D 29 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5874 (tm) REVERT: E 64 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: E 176 GLU cc_start: 0.7116 (tp30) cc_final: 0.6586 (tm-30) REVERT: E 244 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: F 14 LYS cc_start: 0.7067 (mtmp) cc_final: 0.6829 (mppt) REVERT: F 38 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: F 60 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.5811 (m-40) REVERT: F 95 GLN cc_start: 0.6959 (mp10) cc_final: 0.6618 (mp-120) REVERT: F 183 MET cc_start: 0.6558 (mmm) cc_final: 0.6155 (mmm) REVERT: F 189 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6182 (pt0) REVERT: F 281 CYS cc_start: 0.7623 (m) cc_final: 0.7359 (m) REVERT: G 19 TRP cc_start: 0.6389 (t60) cc_final: 0.5974 (t60) outliers start: 49 outliers final: 28 residues processed: 258 average time/residue: 1.2135 time to fit residues: 341.9734 Evaluate side-chains 258 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.0060 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 0.0770 chunk 160 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN A 15 ASN C 71 HIS C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13590 Z= 0.223 Angle : 0.574 11.407 18498 Z= 0.303 Chirality : 0.041 0.169 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.280 57.478 1952 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 3.56 % Allowed : 18.66 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1773 helix: 1.91 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 127 HIS 0.002 0.001 HIS Z 71 PHE 0.014 0.001 PHE F 47 TYR 0.024 0.002 TYR A 73 ARG 0.002 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7722 (t) cc_final: 0.7451 (p) REVERT: Y 47 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (mtmt) REVERT: Y 58 MET cc_start: 0.7792 (mmm) cc_final: 0.7513 (mmp) REVERT: Y 125 ASP cc_start: 0.7153 (m-30) cc_final: 0.6091 (m-30) REVERT: Y 244 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7452 (ttpp) REVERT: Z 54 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7309 (ttm170) REVERT: Z 66 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6903 (mt0) REVERT: Z 94 GLU cc_start: 0.7321 (tt0) cc_final: 0.6987 (tt0) REVERT: Z 187 PHE cc_start: 0.7176 (t80) cc_final: 0.6908 (t80) REVERT: A 55 ASN cc_start: 0.7797 (p0) cc_final: 0.7532 (p0) REVERT: B 26 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7077 (mm-30) REVERT: C 38 GLU cc_start: 0.8538 (tt0) cc_final: 0.8151 (tt0) REVERT: C 61 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7019 (p0) REVERT: C 129 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7857 (m) REVERT: D 29 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5939 (tm) REVERT: E 176 GLU cc_start: 0.7061 (tp30) cc_final: 0.6567 (tm-30) REVERT: E 244 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7858 (ttpp) REVERT: F 14 LYS cc_start: 0.7063 (mtmp) cc_final: 0.6821 (mppt) REVERT: F 38 GLU cc_start: 0.8650 (tt0) cc_final: 0.8220 (tt0) REVERT: F 95 GLN cc_start: 0.6951 (mp10) cc_final: 0.6613 (mp-120) REVERT: F 183 MET cc_start: 0.6583 (mmm) cc_final: 0.6262 (mmm) REVERT: F 189 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: F 281 CYS cc_start: 0.7608 (m) cc_final: 0.7336 (m) REVERT: G 19 TRP cc_start: 0.6399 (t60) cc_final: 0.5968 (t60) outliers start: 49 outliers final: 32 residues processed: 261 average time/residue: 1.2080 time to fit residues: 345.1568 Evaluate side-chains 258 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 147 optimal weight: 0.0980 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 60 ASN Z 189 GLN A 15 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13590 Z= 0.207 Angle : 0.566 11.971 18498 Z= 0.298 Chirality : 0.041 0.162 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.209 59.092 1952 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.49 % Allowed : 18.74 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1773 helix: 1.99 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 127 HIS 0.002 0.001 HIS Z 71 PHE 0.013 0.001 PHE F 47 TYR 0.022 0.002 TYR A 73 ARG 0.002 0.000 ARG Z 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7717 (t) cc_final: 0.7446 (p) REVERT: Y 47 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7231 (mtmt) REVERT: Y 58 MET cc_start: 0.7786 (mmm) cc_final: 0.7501 (mmp) REVERT: Y 125 ASP cc_start: 0.7134 (m-30) cc_final: 0.6699 (m-30) REVERT: Y 244 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7244 (ttpp) REVERT: Z 66 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6892 (mt0) REVERT: Z 94 GLU cc_start: 0.7309 (tt0) cc_final: 0.6968 (tt0) REVERT: Z 187 PHE cc_start: 0.7114 (t80) cc_final: 0.6848 (t80) REVERT: B 26 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 38 GLU cc_start: 0.8519 (tt0) cc_final: 0.8136 (tt0) REVERT: C 61 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6966 (p0) REVERT: C 129 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7844 (m) REVERT: D 29 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5805 (tm) REVERT: E 125 ASP cc_start: 0.7113 (m-30) cc_final: 0.6539 (m-30) REVERT: E 176 GLU cc_start: 0.6952 (tp30) cc_final: 0.6426 (tm-30) REVERT: E 244 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7851 (ttpp) REVERT: F 14 LYS cc_start: 0.7050 (mtmp) cc_final: 0.6806 (mppt) REVERT: F 38 GLU cc_start: 0.8639 (tt0) cc_final: 0.8238 (tt0) REVERT: F 95 GLN cc_start: 0.6945 (mp10) cc_final: 0.6607 (mp-120) REVERT: F 183 MET cc_start: 0.6633 (mmm) cc_final: 0.6325 (mmm) REVERT: F 189 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6161 (pt0) REVERT: F 281 CYS cc_start: 0.7614 (m) cc_final: 0.7352 (m) REVERT: G 19 TRP cc_start: 0.6425 (t60) cc_final: 0.5993 (t60) outliers start: 48 outliers final: 31 residues processed: 264 average time/residue: 1.1970 time to fit residues: 345.5588 Evaluate side-chains 258 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 162 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 172 ASN C 98 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13590 Z= 0.249 Angle : 0.601 12.803 18498 Z= 0.315 Chirality : 0.042 0.179 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.287 58.899 1952 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 3.12 % Allowed : 19.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1773 helix: 1.90 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 127 HIS 0.002 0.001 HIS B 140 PHE 0.015 0.001 PHE F 47 TYR 0.026 0.002 TYR D 73 ARG 0.002 0.000 ARG E 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: Y 22 SER cc_start: 0.7730 (t) cc_final: 0.7448 (p) REVERT: Y 47 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7214 (mtmt) REVERT: Y 58 MET cc_start: 0.7796 (mmm) cc_final: 0.7505 (mmp) REVERT: Y 125 ASP cc_start: 0.7104 (m-30) cc_final: 0.6664 (m-30) REVERT: Y 244 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7455 (ttpp) REVERT: Z 94 GLU cc_start: 0.7316 (tt0) cc_final: 0.6976 (tt0) REVERT: Z 187 PHE cc_start: 0.7307 (t80) cc_final: 0.7036 (t80) REVERT: B 26 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 38 GLU cc_start: 0.8537 (tt0) cc_final: 0.8170 (tt0) REVERT: C 61 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6936 (p0) REVERT: C 129 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7864 (m) REVERT: D 29 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5815 (tm) REVERT: E 125 ASP cc_start: 0.7142 (m-30) cc_final: 0.6588 (m-30) REVERT: E 176 GLU cc_start: 0.6962 (tp30) cc_final: 0.6457 (tm-30) REVERT: E 244 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (ttpp) REVERT: F 38 GLU cc_start: 0.8652 (tt0) cc_final: 0.8220 (tt0) REVERT: F 95 GLN cc_start: 0.6949 (mp10) cc_final: 0.6586 (mp-120) REVERT: F 183 MET cc_start: 0.6653 (mmm) cc_final: 0.6321 (mmm) REVERT: F 189 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6160 (pt0) REVERT: F 281 CYS cc_start: 0.7609 (m) cc_final: 0.7343 (m) REVERT: G 19 TRP cc_start: 0.6393 (t60) cc_final: 0.5960 (t60) outliers start: 43 outliers final: 29 residues processed: 253 average time/residue: 1.2447 time to fit residues: 344.5152 Evaluate side-chains 255 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 161 SER Chi-restraints excluded: chain Y residue 162 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 17 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 180 ASN ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 189 GLN B 172 ASN C 108 ASN ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078402 restraints weight = 17861.570| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.68 r_work: 0.2908 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13590 Z= 0.181 Angle : 0.555 12.419 18498 Z= 0.291 Chirality : 0.040 0.164 2226 Planarity : 0.005 0.087 2328 Dihedral : 5.067 59.434 1952 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 19.61 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1773 helix: 2.06 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 138 HIS 0.002 0.000 HIS Z 71 PHE 0.013 0.001 PHE C 47 TYR 0.018 0.001 TYR D 73 ARG 0.001 0.000 ARG Z 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5892.55 seconds wall clock time: 104 minutes 47.00 seconds (6287.00 seconds total)